Understanding the origin of phonon modes of highly efficient electro-optic crystals is very important for designing materials and for optimizing their photonic applications. Here we investigate the origin of phonon modes in the 0.1–15 THz range of the benchmark electro-optic OH1 (2-(3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene)malononitrile) crystal, interesting due to its large electro-optic coefficient and high THz-wave generation efficiency. The phonon modes (and vibrational absorption properties) of OH1 crystals are evaluated theoretically by periodic density functional theory and also experimentally by THz absorption spectroscopy. The theoretical calculations are well-matched with experimental results. The THz absorption properties are highly anisotropic; the amplitude of vibrational absorption is largest along the polar c-axis compared to the other two crystallographic axes. For comparison, vibrational absorption modes of the OH1 molecule in gas phase are also calculated. The calculated vibrational absorption spectrum of OH1 crystalline powder appears similar to that of the OH1 molecule in gas phase. However, the molecular vibrational motions in crystalline state are coupled motions of vibrational motions in gas phase. Interestingly, the vibrational mode of the torsion of the O-H bond with the largest absorption strength in gas phase is in crystal inhibited due to the crystal field effect. The origin of intense phonon modes of OH1 crystals is mainly related to relatively strong distortions of the push-pull -conjugated system including electron donor and acceptor groups.